BtaINT0128920 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018855 | SCAF4
Description
SR-related CTD-associated factor 4 [Source:HGNC Symbol;Acc:HGNC:19304]
Coordinates
chr1:3075007-3076848:+
Coord C1 exon
chr1:3075007-3075168
Coord A exon
chr1:3075169-3076712
Coord C2 exon
chr1:3076713-3076848
Length
1544 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAG
5' ss Score
7.98
3' ss Seq
CATGTTTTTTCACATAACAGAGT
3' ss Score
5.85
Exon sequences
Seq C1 exon
TGTAAACCAGAATACAAGGTTCCAGGATTATATGTAATCGACTCAATTGTGCGACAGTCTCGTCATCAGTTTGGAACTGATAAAGATGTTTTTGGGCCAAGATTCTCTAAAAACATAACTGCCACATTCCAATATCTGTATCTTTGTCCATCTGAAGATAAG
Seq A exon
GTATAGTTTATAATTTTTAAATTAAACTTGTATTCTTACTCTATTCTTAAATGTATATTAGGTATTTAAAGCCTACTGTATTATTAGAAAGGTAATCACATAGTGATCTCTGTGAACTTGAAACAAAACCCAGTTTTTTTCTATAGTAGTCATATCTATTTTCTTGTGAAGTCCTTCAGAAATGTTGTACTTTTGAAATACAAAAGGAGCATCAGTTCAGTTCAGTCGCTCAGTCGTGTCTGACTCTTTGAAACCCCATGAGTCGCAGCACACCAGGCCTCCCTGTCTATCACCAACTCCCGGAGTTCACCCAAACTCAACGTCCATCGAGTCGGCGATGCCGTCCAGCCATCTCATCCTCTGTCATCCCCTTCTCCTGCACCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCACATGAGGTGGCCAAAGTATTGGAGTTTCAGCTTTAGCATCAGTCCTTCCAAAGAACACCCAGGACTGATCGCCTTTAGAATGGACTGGTTGGATCTCCTTGCAGTTCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCAGCACTCAGCTTTCTTCACAGTCCAACTCTCACATCCATACATGACCACTGGACAAAAAAAAGGAGCATCATCTTTCTTTAAAGAAAACATTATTAGAAAGATTTCTTGTGACTGAATGGTAAAGAAATTCTGCAGTAGAGGAGGACAGTGCTTATCTCAAATTGTTGTTTATTCCAGAAGGAAGGGACCAATCATTGACTTTCCCCATCATATAGAGATGTTGAAGTATAAATGATATTCATTAGCAATCAGACTACTGTATTTAATTCCTCACATTTATAGCTGGTTTTACTCTGTACTATAAAAAGATAGAAAAACATAGACAAGAAACTAGACTCTAATAGATAGGAGAAATACACTGGTAAGCTCAGAATAACAAAGACTAGAGCCTGTATAATAAAGGACATATGAATTCGCATGTTATGGATTCTCTGTATTCTTGGAGGAATGCTCTTGTGGGAAAGATATACAAGAGAAGAGTTCATTCCTAGAGGAGGAGATAAGAGTTGTAACCATGAATAACACATTTTCTCTGGATCTCCTTCAAATTTGGTAACCCACAAAACAACTTACCTAGCAATTAGAGGCCAGTTAATTGTGTTAAATATTTTAACTATTAAAATCATCCTGGATTTTACTCTTCTTAGATAACTGAATTTTTTGGTTTCTTTGTAATCATAAATATGAAAATTTCAAGTAATTCTAATGCATTTCTTTTGACTCTCTAGGTTAATTTTTTGTTTTTTTTCTCTCCCTGTTTCTTACCCTGGATTACACTACTGAAGGAAGGCCAGTTAGAGTAGTTTAATGAGGCTGTAATTCTGATGATAGATTGTTTTCTAACAGATATAGCATGGAAATGTTAGCCTGTGGTGTTTTGTTCTCTCTTTTCATAAGAGGTATAATTATTTATGCTAATACTTATTATATATTCATGTTTTTTCACATAACAG
Seq C2 exon
AGTAAAATAGTTCGTGTATTGAACCTTTGGCAAAAAAATGGAGTATTCAAAATTGAAATTATTCAGCCTCTTTTGGACATGGCAGCAGGAACCAGTAATGCTGCTCCAGTAACAGAAAATGTTACTAATAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018855:ENSBTAT00000025104:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.283
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PU(72.7=88.9)
A:
NA
C2:
PF048188=CTD_bind=PD(24.2=34.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTAAACCAGAATACAAGGTTCCAGG
R:
TAACATTTTCTGTTACTGGAGCAGC
Band lengths:
286-1830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development